rs748809573
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4BP6BS2
The NM_016599.5(MYOZ2):c.313C>T(p.Pro105Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000217 in 1,613,896 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P105R) has been classified as Uncertain significance.
Frequency
Consequence
NM_016599.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYOZ2 | NM_016599.5 | c.313C>T | p.Pro105Ser | missense_variant | 4/6 | ENST00000307128.6 | |
MYOZ2 | XM_006714234.5 | c.313C>T | p.Pro105Ser | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOZ2 | ENST00000307128.6 | c.313C>T | p.Pro105Ser | missense_variant | 4/6 | 1 | NM_016599.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 151976Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251260Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135776
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461802Hom.: 1 Cov.: 35 AF XY: 0.0000165 AC XY: 12AN XY: 727202
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152094Hom.: 0 Cov.: 31 AF XY: 0.0000404 AC XY: 3AN XY: 74338
ClinVar
Submissions by phenotype
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 03, 2024 | The p.P105S variant (also known as c.313C>T), located in coding exon 3 of the MYOZ2 gene, results from a C to T substitution at nucleotide position 313. The proline at codon 105 is replaced by serine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Hypertrophic cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 10, 2020 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at